For Luca Antognoli, subterranean spaces like the Cloaca Maxima offer clues about how this city grew to rule an empire from the edge of Scotland to Baghdad, leaving its imprint indelibly on Western history.

A rivulet coming from the darkness flows down the rubble. Someone asks if it's dirty or clean. "It's very dirty," Luca says, eyeing the opening beyond, "but very important."

The cloaca, originally an open drain, was intentionally buried during the time of the Roman Republic, but most of what underlies Rome is there accidentally, buried by two millennia of sedimentation and urban growth.

"Rome has been rising for 3,000 years," says Darius Arya, an archaeologist and director of the American Institute for Roman Culture. Much of Rome is situated in a floodplain, including the modern city center, known in antiquity as Campus Martius, at a bend of the Tiber River. Although the Romans put up levees, the city still flooded periodically, so they built upward, laying new structures and streets on earlier ones. "It was cost-effective, and it worked," Arya says. "We see the Romans jacking their city up two meters [6.5 feet] at a time, raising themselves above the water but also burying their past."

Today the city sits on layers of history 45 feet (14 meters) deep in places. But ironically, while the beguiling truth of Rome is that you can dig a hole anywhere within the 12-mile (19-kilometer) ring of walls that once enclosed the ancient city and find something of interest, comparatively little of this buried city has been excavated.

"I don't imagine more than 10 percent has been documented," Robert Coates-Stevens says. An archaeology fellow with the British School at Rome, Coates-Stevens has been trying for a decade to piece together the topography of ancient Rome. During the 1800s, the Roman Forum was dug out—work that continues—but most ancient structures are still trapped under the traffic-clogged streets and office buildings of the contemporary city. "It's a heady feeling," Coates-Stevens says, "to think that all this still lies beneath our feet awaiting discovery."

In the 1920s and '30s, seized with this kind of excitement, Benito Mussolini razed sections of Rome's historic center, where medieval and Renaissance houses stood, to reveal the layers below—specifically anything dating back to the time of Emperor Augustus. (Mussolini liked to compare himself to Augustus and equated fascism with Pax Romana, the time of peace ushered in by Augustus.) By the 1980s this big-hole approach to archaeology had fallen out of favor, in part because of the financial challenge of protecting the ruins Mussolini had exposed from acid rain, smog, and vandalism. But curiosity about Rome is eternal, and so the vanguard of archaeology has shifted: Archaeologists, and the speleologists they employ, are exploring ancient spaces from below, leaving the surface undisturbed.